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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGCCCTGCCCACGCTCACGGACGACCTCATCGAACTCATGATGCAGCCGCCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAGgtgcgcggcgccccccccatcccctttgcaaacgacgacggggggcaatttgctttcccccaatctgaatcggaacgtgactcgtcaggcgagcgtagcg...

Basic information

species Zea mays
transcript GRMZM2G134747_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G134747_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os10g33270.1 (Oryza sativa), 5'ss of exon 1
CGGCCCTGCCCACGCTCACGGACGACCTCATCGAACTCATGATGCAGCCGCCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAGgtgc--gcggcgccccccccatcccct--ttgcaaacgacgacggggggcaatttgctttcccccaatctgaatcggaacgtgactcgtc-aggcgagcgtagcg
||||| ||||   |||||| ||||||||| |||  ||||||||| ||||||| ||||| |||||||||||  |||||||||||||||||||||| |||||||||   |  |  |||| || |||| |    | |    ||   |     |||||   | || ||   ||||| ||  |||   ||  ||  | ||   | |    
CGGCCGTGCCGGGGCTCACCGACGACCTCGTCGCGCTCATGATGGAGCCGCCGTTCCGCTCCTACCACCCGGACATCGTCCACGAGCCCGCCATCTACAGgtgcctcctccttcccctccctcccatggccgtaccgtactctgcttctcaattgagtctcgcc---tctgattccaaaccatacatgttgatgctttccttt--
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|211047254|gb|FL125328.1|FL125328
EST:     CCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAG                         ATTGAATGAAGCTGTTATGCATTTTGGAAGAGAGC
genomic: CCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAGgtgcgcggcg ... ttgctcacagATTGAATGAAGCTGTTATGCATTTTGGA-GAGAGC
EST: gi|7844018|gb|AW787345.1|AW787345
EST:     CCCTTCCGGTCCTACCACCTCAACATCGTCCACGAGCCCGCCATTTACAG                         ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAA
genomic: CCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAGgtgcgcggcg ... ttgctcacagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAA
EST: gi|211047251|gb|FL125325.1|FL125325
EST:     CCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAG                         ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAA
genomic: CCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAGgtgcgcggcg ... ttgctcacagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAA
EST: gi|211044297|gb|FL125320.1|FL125320
EST:     CCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAG                         ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAA
genomic: CCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAGgtgcgcggcg ... ttgctcacagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAA
EST: gi|60400889|gb|DN233696.1|DN233696
EST:     CCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAG                         ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAA
genomic: CCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAGgtgcgcggcg ... ttgctcacagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAA
EST: gi|211469684|gb|FL432027.1|FL432027
EST:     CCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAG                         ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAA
genomic: CCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAGgtgcgcggcg ... ttgctcacagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAA
EST: gi|211044290|gb|FL125313.1|FL125313
EST:     CCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAG                         ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAA
genomic: CCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAGgtgcgcggcg ... ttgctcacagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAA
EST: gi|211044292|gb|FL125315.1|FL125315
EST:     CCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAG                         ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAA
genomic: CCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAGgtgcgcggcg ... ttgctcacagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAA
EST: gi|31441069|gb|CD510500.1|CD510500
EST:     CCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAG                         ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAA
genomic: CCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAGgtgcgcggcg ... ttgctcacagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAA
EST: gi|22542458|gb|BU092896.1|BU092896
EST:     CCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAG                         ATTGATATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCA
genomic: CCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAGgtgcgcggcg ... ttgctcacagATTGA-ATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCA
EST: gi|211191597|gb|FL255435.1|FL255435
EST:     CCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAG                         ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAA
genomic: CCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAGgtgcgcggcg ... ttgctcacagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAA
EST: gi|78544325|gb|DV621823.1|DV621823
EST:     CCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAG                         ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAA
genomic: CCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAGgtgcgcggcg ... ttgctcacagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAA
EST: gi|211047250|gb|FL125324.1|FL125324
EST:     CCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAG                         ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAA
genomic: CCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAGgtgcgcggcg ... ttgctcacagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAA
EST: gi|26457359|gb|CA828942.1|CA828942
EST:     CCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAG                         ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAA
genomic: CCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAGgtgcgcggcg ... ttgctcacagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAA
EST: gi|31405717|gb|CD484449.1|CD484449
EST:     CCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAG                         ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAA
genomic: CCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAGgtgcgcggcg ... ttgctcacagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAA
EST: gi|60399029|gb|DN231845.1|DN231845
EST:     CCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAG                         ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAA
genomic: CCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAGgtgcgcggcg ... ttgctcacagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAA
EST: gi|211044293|gb|FL125316.1|FL125316
EST:     CCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAG                         ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAA
genomic: CCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAGgtgcgcggcg ... ttgctcacagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAA
EST: gi|211047249|gb|FL125323.1|FL125323
EST:     CCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAG                         ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAA
genomic: CCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAGgtgcgcggcg ... ttgctcacagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAA
EST: gi|12046752|gb|BF728891.1|BF728891
EST:     CCCTTCCGGTCCTACCACCTCAACATCGTCCACGAGCCCGCCATTTACAG                         ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAA
genomic: CCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAGgtgcgcggcg ... ttgctcacagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAA
EST: gi|31611770|gb|CD568392.1|CD568392
EST:     CCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAG                         ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAA
genomic: CCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAGgtgcgcggcg ... ttgctcacagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAA
EST: gi|30032230|gb|CB834081.1|CB834081
EST:     CCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAG                         ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAA
genomic: CCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAGgtgcgcggcg ... ttgctcacagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAA
EST: gi|211044299|gb|FL125322.1|FL125322
EST:     CCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAG                         ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAA
genomic: CCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAGgtgcgcggcg ... ttgctcacagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAA
EST: gi|31406273|gb|CD485005.1|CD485005
EST:     CCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAG                         ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAA
genomic: CCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAGgtgcgcggcg ... ttgctcacagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAA
EST: gi|7844445|gb|AW787667.1|AW787667
EST:     CCCTTCCGGTCCTACCACCTCAACATCGTCCACGAGCCCGCCATTTACAG                         ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAA
genomic: CCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAGgtgcgcggcg ... ttgctcacagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAA
EST: gi|149011217|gb|EE042296.2|EE042296
EST:     CCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAG                         ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAA
genomic: CCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAGgtgcgcggcg ... ttgctcacagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAA
EST: gi|7844017|gb|AW787344.1|AW787344
EST:     CCCTTCCGGTCCTACCACCTCAACATCGTCCACGAGCCCGCCATTTACAG                         ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAA
genomic: CCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAGgtgcgcggcg ... ttgctcacagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 97

CGGCCCTGCCCACGCTCACGGACGACCTCATCGAACTCATGATGCAGCCGCCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAGgtgcgcggcg ... ttgctcacagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 190

CGGCCCTGCCCACGCTCACGGACGACCTCATCGAACTCATGATGCAGCCGCCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAGgtgcgcggcg ... ttgctcacagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 213

CGGCCCTGCCCACGCTCACGGACGACCTCATCGAACTCATGATGCAGCCGCCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAGgtgcgcggcg ... ttgctcacagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 152

CGGCCCTGCCCACGCTCACGGACGACCTCATCGAACTCATGATGCAGCCGCCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAGgtgcgcggcg ... ttgctcacagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAAT


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGCCCTGCCCACGCTCACGGACGACCTCATCGAACTCATGATGCAGCCGCCCTTCCGGTCCTACCACCCCAACATCGTCCACGAGCCCGCCATTTACAGgtgcgcggcgccccccccatcccctttgcaaacgacgacggggggcaatttgctttcccccaatctgaatcggaacgtgactcgtcaggcgagcgtagcg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccccccc